I don't follow your question 100% of the way but I think I got enough to give you an answer. If the money you spent fixing the property was for major improvements such as a kitchen remodel, a new roof etc. It is depreciated over several years instead of being immediately deductible like a repair on a toilet or your irrigation system would be.
I am not sure why a rental property is being listed on Schedule C. It should be on Schedule E (putting it on Schedule C would cause you pay self-employment taxes).
If you put $20,000 into the property as repairs/renovations in 2017, how much of it is deductible in 2017 depends upon the type of work done and the timing in 2017 (the new tax law had some retroactive impact for qualifying work done at the end of the year).
Also, how much of the repairs/renovations are deductible depends upon whether the work is being done on the rental portion of the fourplex or on your personal residence. The work done on your personal residence is not deductible, but will increase your basis in the property.
There are just so many factors in play to give you an exact answer without knowing all the details
One possible scenario is for you getting the same amount of money back is that you are making over $150,000 and not getting an immediate benefit from your real estate activities(losses are being carried forward).
Another scenario is that the improvements are being capitalized and you are getting the $20,000 benefit over several years and not in the current year.
Another scenario is that you are already getting 100% of your withholding back; of $6,000. Therefore, there is no more that you can get back.
Another scenario is that your accountant was just guessing your refund - did you explain to him that you make more repairs/improvements this year? what was his response
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